Molecular analysis of the interaction between Olea europaea and the biotrophic fungus Spilocaea oleagina

Confronting stresses affecting olive cultivation from the holobiont perspective

The holobiont concept has revolutionized our understanding of plant-associated microbiomes and their significance for the development, fitness, growth and resilience of their host plants. The olive tree holds an iconic status within the Mediterranean Basin. Innovative changes introduced in olive cropping systems, driven by the increasing demand of its derived products, are not only modifying the traditional landscape of this relevant commodity but may also imply that either traditional or emerging stresses can affect it in ways yet to be thoroughly investigated. Incomplete information is currently available about the impact of abiotic and biotic pressures on the olive holobiont, what includes the specific features of its associated microbiome in relation to the host's structural, chemical, genetic and physiological traits. This comprehensive review consolidates the existing knowledge about stress factors affecting olive cultivation and compiles the information available of the microbiota associated with different olive tissues and organs. We aim to offer, based on the existing evidence, an insightful perspective of diverse stressing factors that may disturb the structure, composition and network interactions of the olive-associated microbial communities, underscoring the importance to adopt a more holistic methodology. The identification of knowledge gaps emphasizes the need for multilevel research approaches and to consider the holobiont conceptual framework in future investigations. By doing so, more powerful tools to promote olive's health, productivity and resilience can be envisaged. These tools may assist in the designing of more sustainable agronomic practices and novel breeding strategies to effectively face evolving environmental challenges and the growing demand of high quality food products.

NGS transcriptomic analysis uncovers the possible resistance mechanisms of olive to Spilocea oleagina leaf spot infection

Spilocea oleagina is a dangerous obligate fungal pathogen of olive, feared in the Mediterranean countries, causing Peacock's eye or leaf spot infection, which can lead to a serious yield loss of approximately 20% or higher depending on climatic conditions. Coping with this disease is much more problematic for organic farms. To date, knowledge on the genetic control of possible mechanisms of resistance/low susceptibility is quite limited. In this work, comparative transcriptomic analysis (RNA-seq) was conducted in leaf tissues of a low susceptible cultivar Koroneiki and a high susceptible cultivar Nocellara del Belice, both tested in the field using the NaOH test, considering two stages-"zero sign of disease" and "evident sign of infection". Cultivars showed a very large number of differentially expressed genes (DEGs) in both stages. 'Koroneiki' showed an extensive hormonal crosstalk, involving Abscisic acid (ABA) and ethylene synergistically acting with Jasmonate, with early signaling of the disease and remarkable defense responses against Spilocea through the over-expression of many resistance gene analogs or pathogenesis-related (PR) genes: non-specific lipid-transfer genes (nsLTPs), LRR receptor-like serine/threonine-protein kinase genes, GDSL esterase lipase, defensin Ec-AMP-D2-like, pathogenesis-related leaf protein 6-like, Thaumatin-like gene, Mildew resistance Locus O (MLO) gene, glycine-rich protein (GRP), MADS-box genes, STH-21-like, endochitinases, glucan endo-1,3-beta-glucosidases, and finally, many proteinases. Numerous genes involved in cell wall biogenesis, remodeling, and cell wall-based defense, including lignin synthesis, were also upregulated in the resistant cultivar, indicating the possible role of wall composition in disease resistance. It was remarkable that many transcription factors (TS), some of which involved in Induced Systemic Resistance (ISR), as well as some also involved in abiotic stress response, were found to be uniquely expressed in 'Koroneiki', while 'Nocellara del Belice' was lacking an effective system of defense, expressing genes that overlap with wounding responses, and, to a minor extent, genes related to phenylpropanoid and terpenoid pathways. Only a Thaumatin-like gene was found in both cultivars showing a similar expression. In this work, the genetic factors and mechanism underlying the putative resistance trait against this fungal pathogen were unraveled for the first time and possible target genes for breeding resistant olive genotypes were found.

Olive leaf spot caused by Venturia oleaginea: An updated review

Olive leaf spot (OLS) caused by Venturia oleaginea is widespread in all olive-growing areas and continents, where can cause severe yield losses. The disease is often underestimated for the difficulty to reveal early leaf symptoms and for the pathogen-induced phylloptosis, which creates the illusion of healthy and restored plants. The present review provide updated information on taxonomy, pathogen life style and cycle, epidemiology, diagnosis, and control. Application of copper-based fungicides is the main method to control OLS. However, the regulation 2009/1107 of the European Commission include these fungicides in the list of substances candidates for substitution. It is therefore urgent to find alternative control strategies especially for organic agriculture. Among new approaches/strategies for controlling OLS, promising results have been obtained using nanotechnology, endophytic microbes, and biostimulants.

Laminarin Induces Defense Responses and Efficiently Controls Olive Leaf Spot Disease in Olive

Olive leaf spot (OLS) caused by Fusicladiumoleagineum is mainly controlled using copper fungicides. However, the replacement of copper-based products with eco-friendly alternatives is a priority. The use of plant resistance-inducers (PRIs) or biological control agents (BCAs) could contribute in this direction. In this study we investigated the potential use of three PRIs (laminarin, acibenzolar-S-methyl, harpin) and a BCA (Bacillus amyloliquefaciens FZB24) for the management of OLS. The tested products provided control efficacy higher than 68%. In most cases, dual applications provided higher (p < 0.05) control efficacies compared to that achieved by single applications. The highest control efficacy of 100% was achieved by laminarin. Expression analysis of the selected genes by RT-qPCR revealed different kinetics of induction. In laminarin-treated plants, for most of the tested genes a higher induction rate (p < 0.05) was observed at 3 days post application. Pal, Lox, Cuao and Mpol were the genes with the higher inductions in laminarin-treated and artificially inoculated plants. The results of this study are expected to contribute towards a better understanding of PRIs in olive culture and the optimization of OLS control, while they provide evidence for potential contributions in the reduction of copper accumulation in the environment.

Defining the root endosphere and rhizosphere microbiomes from the World Olive Germplasm Collection

The bacterial and fungal communities from the olive (Olea europaea L.) root systems have not yet been simultaneously studied. We show in this work that microbial communities from the olive root endosphere are less diverse than those from the rhizosphere. But more relevant was to unveil that olive belowground communities are mainly shaped by the genotype of the cultivar when growing under the same environmental, pedological and agronomic conditions. Furthermore, Actinophytocola, Streptomyces and Pseudonocardia are the most abundant bacterial genera in the olive root endosphere, Actinophytocola being the most prevalent genus by far. In contrast, Gp6, Gp4, Rhizobium and Sphingomonas are the main genera in the olive rhizosphere. Canalisporium, Aspergillus, Minimelanolocus and Macrophomina are the main fungal genera present in the olive root system. Interestingly enough, a large number of as yet unclassified fungal sequences (class level) were detected in the rhizosphere. From the belowground microbial profiles here reported, it can be concluded that the genus Actinophytocola may play an important role in olive adaptation to environmental stresses. Moreover, the huge unknown fungal diversity here uncovered suggests that fungi with important ecological function and biotechnological potential are yet to be identified.

Fungal Communities Associated with Peacock and Cercospora Leaf Spots in Olive

Venturia oleaginea and Pseudocercospora cladosporioides are two of the most important olive fungal pathogens causing leaf spots: peacock spot, and cercosporiosis, respectively. In the present study, fungal communities associated with the presence of these pathogens were investigated. Overall, 300 symptomatic and asymptomatic trees from different cultivars were sampled from Alentejo, Portugal. A total of 788 fungal isolates were obtained and classified into 21 OTUs; Ascomycota was clearly the predominant phylum (96.6%). Trees from cultivar 'Galega vulgar' showed a significant higher fungal richness when compared to 'Cobrançosa', which in turn showed significant higher values than 'Picual'. Concerning plant health status, symptomatic plants showed significant higher fungal richness, mainly due to the high number of isolates of the pathogens V. oleaginea and P. cladosporioides. In terms of fungal diversity, there were two major groups: ca. 90% of the isolates found in symptomatic plants belonged to V. oleaginea, P. cladosporioides, Chalara sp., and Foliophoma sp. while ca. 90% of the isolates found in asymptomatic plants, belonged to Alternaria sp. and Epicoccum sp. This study highlights the existence of different fungal communities in olive trees, including potential antagonistic organisms that can have a significant impact on diseases and consequently on olive production.

Transcriptional Regulation of Stearoyl-Acyl Carrier Protein Desaturase Genes in Response to Abiotic Stresses Leads to Changes in the Unsaturated Fatty Acids Composition of Olive Mesocarp

In higher plants, the stearoyl-acyl carrier protein desaturase (SAD) catalyzes the first desaturation step leading to oleic acid, which can be further desaturated to linoleic and α-linolenic acids. Therefore, SAD plays an essential role in determining the overall content of unsaturated fatty acids (UFA). We have investigated how SAD genes expression and UFA composition are regulated in olive (Olea europaea) mesocarp tissue from Picual and Arbequina cultivars in response to different abiotic stresses. The results showed that olive SAD genes are transcriptionally regulated by temperature, darkness and wounding. The increase in SAD genes expression levels observed in Picual mesocarp exposed to low temperature brought about a modification in the UFA content of microsomal membrane lipids. In addition, darkness caused the down-regulation of SAD genes transcripts, together with a decrease in the UFA content of chloroplast lipids. The differential role of olive SAD genes in the wounding response was also demonstrated. These data point out that different environmental stresses can modify the UFA composition of olive mesocarp through the transcriptional regulation of SAD genes, affecting olive oil quality.

The transcriptional response to the olive fruit fly (Bactrocera oleae) reveals extended differences between tolerant and susceptible olive (Olea europaea L.) varieties

The olive fruit fly Bactrocera oleae (Diptera: Tephritidae) is the most devastating pest of cultivated olive (Olea europaea L.). Intraspecific variation in plant resistance to B. oleae has been described only at phenotypic level. In this work, we used a transcriptomic approach to study the molecular response to the olive fruit fly in two olive cultivars with contrasting level of susceptibility. Using next-generation pyrosequencing, we first generated a catalogue of more than 80,000 sequences expressed in drupes from approximately 700k reads. The assembled sequences were used to develop a microarray layout with over 60,000 olive-specific probes. The differential gene expression analysis between infested (i.e. with II or III instar larvae) and control drupes indicated a significant intraspecific variation between the more tolerant and susceptible cultivar. Around 2500 genes were differentially regulated in infested drupes of the tolerant variety. The GO annotation of the differentially expressed genes implies that the inducible resistance to the olive fruit fly involves a number of biological functions, cellular processes and metabolic pathways, including those with a known role in defence, oxidative stress responses, cellular structure, hormone signalling, and primary and secondary metabolism. The difference in the induced transcriptional changes between the cultivars suggests a strong genetic role in the olive inducible defence, which can ultimately lead to the discovery of factors associated with a higher level of tolerance to B. oleae.

Relative Susceptibility of New Olive Cultivars to Spilocaea oleagina, Colletotrichum acutatum, and Pseudocercospora cladosporioides

The evaluation of the relative susceptibility of new cultivars to the main diseases of a crop is a key point to consider prior to their release to the nursery industry. This study provides a rigorous characterization of the resistance of 15 new olive cultivars and their genitors ('Arbequina,' 'Frantoio,' and 'Picual') to the three main aerial diseases, peacock spot, anthracnose, and cercosporiosis caused by Spilocaea oleagina, Colletotrichum acutatum, and Pseudocercospora cladosporioides, respectively. To do so, developing leaves and detached green-yellowish fruit were inoculated in laboratory tests with S. oleagina and C. acutatum, respectively, using conidial suspensions of both pathogens. Additionally, a previously validated rating scale was used to assess the incidence of leaves with symptoms of S. oleagina or P. cladosporioides and the fruit rot incidence of C. acutatum in the trees for four years under field conditions. As a result, only two of the cultivars were susceptible to peacock spot, most likely because these new cultivars were previously screened for resistance to the disease on previous phases of the breeding program. Conversely, the 15 cultivars were susceptible or moderately susceptible to cercosporiosis. Five of the 15 new cultivars were classified as resistant to anthracnose, with four of them descendants of 'Frantoio' × 'Picual' crosses. In addition, the cultivars resistance to C. acutatum showed a negative linear correlation with the total phenols content of olive oil. This information regarding disease reaction of the new olive cultivars is essential for nursery industry and growers.

Molecular interactions between the olive and the fruit fly Bactrocera oleae

BACKGROUND

The fruit fly Bactrocera oleae is the primary biotic stressor of cultivated olives, causing direct and indirect damages that significantly reduce both the yield and the quality of olive oil. To study the olive-B. oleae interaction, we conducted transcriptomic and proteomic investigations of the molecular response of the drupe. The identifications of genes and proteins involved in the fruit response were performed using a Suppression Subtractive Hybridisation technique and a combined bi-dimensional electrophoresis/nanoLC-ESI-LIT-MS/MS approach, respectively.

RESULTS

We identified 196 ESTs and 26 protein spots as differentially expressed in olives with larval feeding tunnels. A bioinformatic analysis of the identified non-redundant EST and protein collection indicated that different molecular processes were affected, such as stress response, phytohormone signalling, transcriptional control and primary metabolism, and that a considerable proportion of the ESTs could not be classified. The altered expression of 20 transcripts was also analysed by real-time PCR, and the most striking differences were further confirmed in the fruit of a different olive variety. We also cloned the full-length coding sequences of two genes, Oe-chitinase I and Oe-PR27, and showed that these are wound-inducible genes and activated by B. oleae punctures.

CONCLUSIONS

This study represents the first report that reveals the molecular players and signalling pathways involved in the interaction between the olive fruit and its most damaging biotic stressor. Drupe response is complex, involving genes and proteins involved in photosynthesis as well as in the production of ROS, the activation of different stress response pathways and the production of compounds involved in direct defence against phytophagous larvae. Among the latter, trypsin inhibitors should play a major role in drupe resistance reaction.

Factors Affecting Infection and Disease Development on Olive Leaves Inoculated with Fusicladium oleagineum

Infection and development of olive scab disease, caused by Fusicladium oleagineum, were evaluated on detached leaves and potted plants of the susceptible cultivar Picual in growth chambers and a shadehouse. An inoculum dose of 1 × 10⁵ conidia per ml was selected from a range of densities tested, and it was used for all experiments. Infection occurred from 5 to 25°C, and disease severity was the greatest at ~20°C for wetness durations of 12 to 24 h and at ~15°C for longer durations. Based on a generalized form of the Analytis Beta model, the optimum temperature and minimum wetness duration for infection were 15.5°C and 11.9 h. Dry periods ≤78 h immediately after inoculation did not reduce disease incidence but did reduce disease severity. Disease severity was negatively correlated with leaf age. Disease incubation period was positively correlated with leaf age, with a minimum incubation period of 28 days in the youngest leaves. Inoculated plants that were incubated in a growth chamber or in a shadehouse had the same level of infection, but disease severity was lower in plants incubated in the growth chamber because many infections remained latent for 6 months after inoculation. The data in this study will be useful for the development of a forecasting system for olive scab epidemics.

Searching for Moniliophthora perniciosa pathogenicity genes

The basidiomycete Moniliophthora perniciosa is the causal agent of witches' broom disease of Theobroma cacao (cacao). Pathogenesis mechanisms of this hemibiotrophic fungus are largely unknown. An approach to identify putative pathogenicity genes is searching for sequences induced in mycelia grown under in vitro conditions. Using this approach, genes from M. perniciosa induced under limiting nitrogen and light were identified from a cDNA library enriched by suppression subtractive hybridization as potential putative pathogenicity genes. From the 159 identified unique sequences, 59 were annotated and classified by gene ontology. Two sequences were categorized as "Defence genes, Virulence, and Cell response" presumably coding for allergenic proteins, whose homologues from other fungi are inducers of animal or plant defences. Differential gene expression was evaluated by quantitative amplification of reversed transcripts (RT-qPCR) of the putative identified genes coding for the two allergenic proteins (Aspf13 and 88KD), and for the enzymes Arylsulfatase (AS); Aryl-Alcohol Oxidase; Aldo-Keto Reductase (AK); Cytochrome P450 (P450); Phenylalanine Ammonia-Lyase; and Peroxidase from mycelia grown under contrasting N concentrations. All genes were validated for differential expression, except for the putative Peroxidase. The same eight genes were analysed for expression in susceptible plants inoculated with M. perniciosa, and six were induced during the early asymptomatic stage of the disease. In infected host tissues, transcripts of 88KD and AS were found more abundant at the biotrophic phase, while those from Aspf13, AK, PAL, and P450 accumulated at the necrotrophic phase, enabling to suggest that mycelia transition from biotrophic to necrotrophic might occur earlier than currently considered. These sequences appeared to be virulence life-style genes, which encode factors or enzymes that enable invasion, colonization or intracellular survival, or manipulate host factors to benefit the pathogen's own survival in the hostile environment.

Molecular analysis of menadione-induced resistance against biotic stress in Arabidopsis

Menadione sodium bisulphite (MSB) is a water-soluble derivative of vitamin K3, or menadione, and has been previously demonstrated to function as a plant defence activator against several pathogens in several plant species. However, there are no reports of the role of this vitamin in the induction of resistance in the plant model Arabidopsis thaliana. In the current study, we demonstrate that MSB induces resistance by priming in Arabidopsis against the virulent strain Pseudomonas syringae pv. tomato DC3000 (Pto) without inducing necrosis or visible damage. Changes in gene expression in response to 0.2 mm MSB were analysed in Arabidopsis at 3, 6 and 24 h post-treatment using microarray technology. In general, the treatment with MSB does not correlate with other publicly available data, thus MSB produces a unique molecular footprint. We observed 158 differentially regulated genes among all the possible trends. More up-regulated genes are included in categories such as 'response to stress' than the background, and the behaviour of these genes in different treatments confirms their role in response to biotic and abiotic stress. In addition, there is an over-representation of the G-box in their promoters. Some interesting functions are represented among the individual up-regulated genes, such as glutathione S-transferases, transcription factors (including putative regulators of the G-box) and cytochrome P450s. This work provides a wide insight into the molecular cues underlying the effect of MSB as a plant resistance inducer.

Identification by suppression subtractive hybridization of genes expressed in pear (Pyrus spp.) upon infestation with Cacopsylla pyri (Homoptera: Psyllidae)

The molecular interaction between pear tree (Pyrus spp.) and the phloem-feeding psylla Cacopsylla pyri (Linnaeus) was investigated through the construction and characterization of cDNA subtracted libraries. Genes expressed upon insect infestation were identified in the susceptible pear cultivar Bartlett and in the resistant selection NY10355. In both interactions, genes involved in the plant defense response were induced, confirming the observed similarity between the response to pathogens and to insects with piercing/sucking mouthparts. However, the two expression profiles were found to be different, with more genes involved in the response to biotic and abiotic stress being activated in the resistant plant than in the susceptible one. Further characterization of the identified genes could lead to the development of molecular markers associated with tolerance/resistance to pear psylla.

Expression profiling and mapping of defence response genes associated with the barley-Pyrenophora teres incompatible interaction

Barley net- and spot-form of net blotch disease are caused by two formae of the hemibiotrophic fungus Pyrenophora teres (P. t. f. teres and P. t. f. maculata). In the present study, suppression subtractive hybridization (SSH) was used in combination with quantitative real-time reverse transcriptase PCR to identify and profile the expression of defence response (DR) genes in the early stages of both barley-P. teres incompatible and compatible interactions. From a pool of 307 unique gene transcripts identified by SSH, 45 candidate DR genes were selected for temporal expression profiling in infected leaf epidermis. Differential expression profiles were observed for 28 of the selected candidates, which were grouped into clusters depending on their expression profiles within the first 48 h after inoculation. The expression profiles characteristic of each gene cluster were very similar in both barley-P. t. f. teres and barley-P. t. f. maculata interactions, indicating that resistance to both pathogens could be mediated by induction of the same group of DR genes. Chromosomal map locations for 21 DR genes were identified using four doubled-haploid mapping populations. The mapped DR genes were distributed across all seven barley chromosomes, with at least one gene mapping to within 15 cM of another on chromosomes 1H, 2H, 5H and 7H. Additionally, some DR genes appeared to co-localize with loci harbouring known resistance genes or quantitative trait loci for net blotch resistance on chromosomes 6H and 7H, as well as loci associated with resistance to other barley diseases. The DR genes are discussed with respect to their map locations and potential functional role in contributing to net blotch disease resistance.

Genes differentially expressed in Theobroma cacao associated with resistance to witches' broom disease caused by Crinipellis perniciosa

SUMMARY The basidiomycete Crinipellis perniciosa is the causal agent of witches' broom disease of Theobroma cacao (cocoa). Hypertrophic growth of infected buds ('brooms') is the most dramatic symptom, but the main economic losses derive from pod infection. To identify cocoa genes differentially expressed during the early stages of infection, two cDNA libraries were constructed using the suppression subtractive hybridization (SSH) approach. Subtraction hybridization was conducted between cDNAs from infected shoot-tips of the susceptible genotype 'ICS 39' and the resistant 'CAB 214', in both directions. A total of 187 unique sequences were obtained, with 83 from the library enriched for the susceptible 'ICS 39' sequences, and 104 for the resistant 'CAB 214'. By homology search and ontology analyses, the identified sequences were mainly putatively categorized as belonging to 'signal transduction', 'response to biotic and abiotic stress', 'metabolism', 'RNA and DNA metabolism', 'protein metabolism' and 'cellular maintenance' classes. Quantitative reverse transcription amplification (RT-qPCR) of 23 transcripts identified as differentially expressed between genotypes revealed distinct kinetics of gene up-regulation at the asymptomatic stage of the disease. Expression induction in the susceptible 'ICS 39' in response to C. perniciosa was delayed and limited, while in 'CAB 214' there was a quicker and more intense reaction, with two peaks of gene induction at 48 and 120 h after inoculation, corresponding to morphological and biochemical changes previously described during colonization. Similar differences in gene induction were validated for another resistant genotype ('CAB 208') in an independent experiment. Validation of these genes corroborated similar hypothetical mechanisms of resistance described in other pathosystems.